chr4-105213159-G-A

Position:

• chr4-105213159-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001127208.3(TET2):​c.-46-20738G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 151,884 control chromosomes in the GnomAD database, including 6,535 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6535 hom., cov: 32)
• Consequence: TET2 NM_001127208.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

Genes affected

TET2 (HGNC:25941): (tet methylcytosine dioxygenase 2) The protein encoded by this gene is a methylcytosine dioxygenase that catalyzes the conversion of methylcytosine to 5-hydroxymethylcytosine. The encoded protein is involved in myelopoiesis, and defects in this gene have been associated with several myeloproliferative disorders. Two variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]

TET2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TET2	NM_001127208.3	c.-46-20738G>A		intron_variant		ENST00000380013.9	NP_001120680.1
TET2-AS1	NR_126420.1	n.319-35487C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TET2	ENST00000380013.9	c.-46-20738G>A		intron_variant		5	NM_001127208.3	ENSP00000369351	A2

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41939 AN: 151766 Hom.: 6537 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.264

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.276 AC: 41930 AN: 151884 Hom.: 6535 Cov.: 32 AF XY: 0.273 AC XY: 20225 AN XY: 74202

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.259

Alfa AF: 0.326 Hom.: 2414

Bravo AF: 0.265

Asia WGS AF: 0.235 AC: 821 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.72
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6855629; hg19: chr4-106134316;